[2] | 1 | <tool id="gff2bed1" name="GFF-to-BED" version="1.0.1"> |
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| 2 | <description>converter</description> |
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| 3 | <command interpreter="python">gff_to_bed_converter.py $input $out_file1</command> |
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| 4 | <inputs> |
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| 5 | <param format="gff" name="input" type="data" label="Convert this query"/> |
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| 6 | </inputs> |
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| 7 | <outputs> |
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| 8 | <data format="bed" name="out_file1" /> |
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| 9 | </outputs> |
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| 10 | <tests> |
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| 11 | <test> |
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| 12 | <param name="input" value="5.gff" ftype="gff"/> |
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| 13 | <output name="out_file1" file="gff2bed_out.bed"/> |
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| 14 | </test> |
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| 15 | <test> |
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| 16 | <param name="input" value="gff2bed_in2.gff" ftype="gff"/> |
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| 17 | <output name="out_file1" file="gff2bed_out2.bed"/> |
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| 18 | </test> |
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| 19 | </tests> |
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| 20 | <help> |
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| 21 | |
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| 22 | **What it does** |
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| 23 | |
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| 24 | This tool converts data from GFF format to BED format (scroll down for format description). |
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| 25 | |
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| 26 | -------- |
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| 27 | |
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| 28 | **Example** |
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| 29 | |
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| 30 | The following data in GFF format:: |
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| 31 | |
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| 32 | chr22 GeneA enhancer 10000000 10001000 500 + . TGA |
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| 33 | chr22 GeneA promoter 10010000 10010100 900 + . TGA |
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| 34 | |
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| 35 | Will be converted to BED (**note** that 1 is subtracted from the start coordinate):: |
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| 36 | |
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| 37 | chr22 9999999 10001000 enhancer 0 + |
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| 38 | chr22 10009999 10010100 promoter 0 + |
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| 39 | |
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| 40 | ------ |
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| 41 | |
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| 42 | .. class:: infomark |
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| 43 | |
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| 44 | **About formats** |
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| 45 | |
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| 46 | **BED format** Browser Extensible Data format was designed at UCSC for displaying data tracks in the Genome Browser. It has three required fields and several additional optional ones: |
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| 47 | |
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| 48 | The first three BED fields (required) are:: |
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| 49 | |
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| 50 | 1. chrom - The name of the chromosome (e.g. chr1, chrY_random). |
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| 51 | 2. chromStart - The starting position in the chromosome. (The first base in a chromosome is numbered 0.) |
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| 52 | 3. chromEnd - The ending position in the chromosome, plus 1 (i.e., a half-open interval). |
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| 53 | |
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| 54 | The additional BED fields (optional) are:: |
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| 55 | |
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| 56 | 4. name - The name of the BED line. |
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| 57 | 5. score - A score between 0 and 1000. |
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| 58 | 6. strand - Defines the strand - either '+' or '-'. |
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| 59 | 7. thickStart - The starting position where the feature is drawn thickly at the Genome Browser. |
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| 60 | 8. thickEnd - The ending position where the feature is drawn thickly at the Genome Browser. |
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| 61 | 9. reserved - This should always be set to zero. |
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| 62 | 10. blockCount - The number of blocks (exons) in the BED line. |
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| 63 | 11. blockSizes - A comma-separated list of the block sizes. The number of items in this list should correspond to blockCount. |
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| 64 | 12. blockStarts - A comma-separated list of block starts. All of the blockStart positions should be calculated relative to chromStart. The number of items in this list should correspond to blockCount. |
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| 65 | 13. expCount - The number of experiments. |
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| 66 | 14. expIds - A comma-separated list of experiment ids. The number of items in this list should correspond to expCount. |
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| 67 | 15. expScores - A comma-separated list of experiment scores. All of the expScores should be relative to expIds. The number of items in this list should correspond to expCount. |
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| 68 | |
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| 69 | **GFF format** General Feature Format is a format for describing genes and other features associated with DNA, RNA and Protein sequences. GFF lines have nine tab-separated fields:: |
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| 70 | |
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| 71 | 1. seqname - Must be a chromosome or scaffold. |
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| 72 | 2. source - The program that generated this feature. |
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| 73 | 3. feature - The name of this type of feature. Some examples of standard feature types are "CDS", "start_codon", "stop_codon", and "exon". |
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| 74 | 4. start - The starting position of the feature in the sequence. The first base is numbered 1. |
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| 75 | 5. end - The ending position of the feature (inclusive). |
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| 76 | 6. score - A score between 0 and 1000. If there is no score value, enter ".". |
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| 77 | 7. strand - Valid entries include '+', '-', or '.' (for don't know/care). |
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| 78 | 8. frame - If the feature is a coding exon, frame should be a number between 0-2 that represents the reading frame of the first base. If the feature is not a coding exon, the value should be '.'. |
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| 79 | 9. group - All lines with the same group are linked together into a single item. |
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| 80 | |
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| 81 | </help> |
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| 82 | </tool> |
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